Abstract

Abstract
Formal concept analysis (FCA) is largely applied in different areas. However, in some FCA applications the volume of information that needs to be processed can become unfeasible. Thus, the demand for new approaches and algorithms that enable processing large amounts of information is increasing substantially. This article presents a new algorithm for extracting proper implications from high-dimensional contexts. The proposed algorithm, called ImplicPBDD, was based on the Proplm algorithm, and uses a data structure called binary decision diagram (BDD) to simplify the representation of the formal context and enhance the extraction of proper implications. In order to analyze the performance of the ImplicPBDD algorithm, we performed tests using synthetic contexts varying the number of objects, attributes and context density. The experiments show that ImplicPBDD has a better performance-up to 80% faster-than its original algorithm, regardless of the number of attributes, objects and densities

Abstract

Abstract

Abstract
Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante-and postmortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.

Abstract
Bioinformatics Algorithms: Design and Implementation in Python provides a comprehensive book on many of the most important bioinformatics problems, putting forward the best algorithms and showing how to implement them. The book focuses on the use of the Python programming language and its algorithms, which is quickly becoming the most popular language in the bioinformatics field. Readers will find the tools they need to improve their knowledge and skills with regard to algorithm development and implementation, and will also uncover prototypes of bioinformatics applications that demonstrate the main principles underlying real world applications.